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From: Lutz F. <not...@gi...> - 2016-05-27 16:21:24
|
Currently SearchModifications do not encode for separate sites of e.g. a cross-linker.
To circumvent this we could use the same method as we encode the peptide modifications. I.e. encode the cross-linker as one modification that holds the mass and the specificities for one site and have a second 0 mass modification that encodes for the specificities second site of the cross-linker.
E.g. for BS3 alone:
```
<SearchModification fixedMod="false" massDelta="138.06808" residues="S T Y K">
<cvParam cvRef="XLMOD" accession="XL:00001" name="Xlink:BS3"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="138.06808" residues=".">
<SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
</SpecificityRules>
<cvParam cvRef="XLMOD" accession="XL:00001" name="Xlink:BS3"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="0.0" residues="S T Y K">
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="0.0" residues=".">
<SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
</SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0"></cvParam>
</SearchModification>
```
both sides of the cross-linker are linked (the same as in peptide modifications) vi cvterms:
```
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="X">
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="X">
```
For a case with two cross-linker (e.g BS3-d0/BS3-d4) thsi would look like this:
```
<SearchModification fixedMod="false" massDelta="138.06808" residues="S T Y K">
<cvParam cvRef="XLMOD" accession="XL:00001" name="Xlink:BS3"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="138.06808" residues=".">
<SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
</SpecificityRules>
<cvParam cvRef="XLMOD" accession="XL:00001" name="Xlink:BS3"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="0.0" residues="S T Y K">
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="0.0" residues=".">
<SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
</SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="142.09317" residues="S T Y K">
<cvParam cvRef="XLMOD" accession="XL:00005" name="Xlink:BS3:d4"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="1"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="142.09317" residues=".">
<SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
</SpecificityRules>
<cvParam cvRef="XLMOD" accession="XL:00005" name="Xlink:BS3:d4"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="1"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="0.0" residues="S T Y K">
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="1"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="0.0" residues=".">
<SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
</SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="1"></cvParam>
</SearchModification>
```
---
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Reply to this email directly or view it on GitHub:
https://github.com/HUPO-PSI/mzIdentML/issues/30 |
|
From: Lutz F. <lfi...@st...> - 2016-05-27 13:07:31
|
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
|
From: Jones, A. <And...@li...> - 2016-05-27 13:01:13
|
Thanks Lutz – would you mind opening this as an issue on GitHub so we remember to discuss it, but your encoding looks sensible.
Best wishes
Andy
From: Lutz Fischer [mailto:lfi...@st...]
Sent: 27 May 2016 13:24
To: Jones, Andy <jo...@li...>; 'psi...@li...' <psi...@li...>
Subject: Cross-linker Search-modification
Hi Andy,
I am implementing the ProteinDetection (just have another 9000 or so error messages from the validator to go through ...)
But I realised so far I never did write out cross-linker as SearchModification so I got some questions there:
How to encode can link K,S,T,Y and N-terminals?
How to encode the two site of the cross-linker?
I currently address that by (example is BS3) first writing one SearchModification for K,S,T and Y and one for the N-terminal.
For the second site I did write out A acceptor modification of zero-mass - actually again two. one for K,S,T,Y and one for N-terminal.
so for BS3 I have currently following SearchModifications:
<SearchModification fixedMod="false" massDelta="138.06808" residues="S T Y K">
<cvParam cvRef="XLMOD" accession="XL:00001" name="Xlink:BS3"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="138.06808" residues=".">
<SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
</SpecificityRules>
<cvParam cvRef="XLMOD" accession="XL:00001" name="Xlink:BS3"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="0.0" residues="S T Y K">
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="0.0" residues=".">
<SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
</SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0"></cvParam>
</SearchModification>
The modification that denote the same cross-linker are here marked also with the same value for
cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0">
So for two cross-linker (e.g. BS3 and BS3-d0) it would look like this:
<SearchModification fixedMod="false" massDelta="138.06808" residues="S T Y K">
<cvParam cvRef="XLMOD" accession="XL:00001" name="Xlink:BS3"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="138.06808" residues=".">
<SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
</SpecificityRules>
<cvParam cvRef="XLMOD" accession="XL:00001" name="Xlink:BS3"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="0.0" residues="S T Y K">
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="0.0" residues=".">
<SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
</SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="0"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="142.09317" residues="S T Y K">
<cvParam cvRef="XLMOD" accession="XL:00005" name="Xlink:BS3:d4"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="1"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="142.09317" residues=".">
<SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
</SpecificityRules>
<cvParam cvRef="XLMOD" accession="XL:00005" name="Xlink:BS3:d4"></cvParam>
<cvParam cvRef="PSI-MS" accession="MS:1002509" name="cross-link donor" value="1"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="0.0" residues="S T Y K">
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="1"></cvParam>
</SearchModification>
<SearchModification fixedMod="false" massDelta="0.0" residues=".">
<SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002057" name="modification specificity protein N-term"></cvParam>
</SpecificityRules>
<cvParam cvRef="PSI-MS" accession="MS:1002510" name="cross-link acceptor" value="1"></cvParam>
</SearchModification>
In this example the acceptor looks exactly the same for both but e.g. if EDC and BS3 where mixed then the acceptor would differ as well.
Not sure if that would be needed/wanted - but I think that keeps things in line on how it is used for peptide modifications
Currently there seems to be no specification for this in the spec-document and probably would need to be added.
I send this also to the psi-pi mailing list. I assume other people might encounter the same questions.
Best wishes,
Lutz
On 26/05/16 17:21, Jones, Andy wrote:
Hi Lutz,
No these will have to go onto the PDH level. A simple protein ID process is fine, the software doesn’t need to do grouping info. Each Protein group can contain a single protein, with whatever score you want to give it.
DBSequence simply means a database protein, so we don’t put inferred values from the experiment on here.
Best wishes
Andy
From: Lutz Fischer [mailto:lfi...@st...]
Sent: 26 May 2016 17:10
To: Jones, Andy
Subject: mzIdentML +Protein Pair Information
Hi Andy,
Just realized that with the current way to store residue-pair information we force people to do protein grouping - even if all they want to store are a score or FDR for residue pairs.
Would it be sensible to move these to DBSequence? If we take your suggested way and just move it to DBSeqeunce it would still work for residue pairs. Admittedly when it comes to protein pairs it only really makes sense with protein groups.
I have an example without residue and protein pair information - but some trouble with the validator came up - so didn't upload the example yet.
As I am currently struggling a bit with writing out protein-groups, the example is not quite ready and would then also need to pass the validator.
Lutz
--
Lutz Fischer
lfi...@st...<mailto:lfi...@st...>
+44 131 6517057
--
Lutz Fischer
lfi...@st...<mailto:lfi...@st...>
+44 131 6517057
|
|
From: andrewrobertjones <not...@gi...> - 2016-05-26 12:27:06
|
Thanks @germa for this. I added some comments to the document, but there are still a few parts unclear to me. Perhaps we should discuss in detail on our next call --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/25#issuecomment-221856794 |
|
From: Gerhard M. <not...@gi...> - 2016-05-25 14:41:34
|
[CV-terms for PTM, PSM, peptide, protein and protein-group scores.docx](https://github.com/HUPO-PSI/mzIdentML/files/282210/CV-terms.for.PTM.PSM.peptide.protein.and.protein-group.scores.docx) --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/25#issuecomment-221597809 |
|
From: Steffen N. <sne...@ip...> - 2016-05-25 13:28:38
|
Hi, I'd be a bit hesitant to have one term per neutral loss. The Table 2 in http://pubs.acs.org/doi/full/10.1021/ac101825k#tbl2-fn1 contains already >30 neutral losses, and it is not complete ... What about a generic neutral loss that has a value which is a formula ? Yours, Steffen On Di, 2016-05-24 at 15:55 +0200, mayerg97 wrote: > ************ New terms for neutral losses > [Term] > id: MS:1002668 > name: HPO3 neutral loss > def: "Neutral loss of phosphite." [PSI:PI] > is_a: MS:1000336 ! neutral loss > is_a: MS:1002473 ! ion series considered in search > ... > name: CH4OS neutral loss > name: C3H9N neutral loss -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 |
|
From: Eric D. <ede...@sy...> - 2016-05-24 16:01:39
|
Hi Gerhard, many thanks for adjusting this. Regarding the reporter ions, what does “mass resp. type” mean? If there is a value that must be supplied, the term name and definition really should be about that value. Thanks, Eric *From:* mayerg97 [mailto:ger...@ru...] *Sent:* Tuesday, May 24, 2016 6:56 AM *To:* Harald Barsnes; psi...@li...; psi...@li...; psi...@li... *Subject:* Re: [Psidev-ms-dev] PSI-MS: reporter ion cv terms Hi all, how about the following terms? ************ New terms for neutral losses [Term] id: MS:1002668 name: HPO3 neutral loss def: "Neutral loss of phosphite." [PSI:PI] is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1002669 name: CH4OS neutral loss def: "Neutral loss of methanesulfenic acid." [PSI:PI] is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1002670 name: C3H9N neutral loss def: "Neutral loss of C3H9N." [PSI:PI] is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search ************ New terms for reporter ions. The mass resp. type can be specified in the value slot. [Term] id: MS:1002671 name: frag: iTRAQ 4plex reporter ion def: "Standard reporter ion for iTRAQ 4Plex." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1002672 name: frag: iTRAQ 8plex reporter ion def: "Standard reporter ion for iTRAQ 8Plex." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1002673 name: frag: TMT reporter ion def: "Standard reporter ion for TMT." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1002674 name: frag: TMT ETD reporter ion def: "Standard reporter ion for TMT ETD." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type Best regards, Gerhard Am 24.05.2016 um 12:55 schrieb Harald Barsnes: Hi Gerhard, Thanks for adding the neutral losses CV terms. Would be great if you could also add CV terms for the following reporter ions. iTRAQ 4plex: Name: frag: iTRAQ 4plex 114 reporter ion Description: Standard reporter ion for iTRAQ 4Plex 114. Name: frag: iTRAQ 4plex 115 reporter ion Description: Standard reporter ion for iTRAQ 4Plex 115. Name: frag: iTRAQ 4plex 116 reporter ion Description: Standard reporter ion for iTRAQ 4Plex 116. Name: frag: iTRAQ 4plex 117 reporter ion Description: Standard reporter ion for iTRAQ 4Plex 117. iTRAQ 8plex: Name: frag: iTRAQ 8plex 113 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 113. Name: frag: iTRAQ 8plex 114 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 114. Name: frag: iTRAQ 8plex 115 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 115. Name: frag: iTRAQ 8plex 116 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 116. Name: frag: iTRAQ 8plex 117 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 117. Name: frag: iTRAQ 8plex 118 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 118. Name: frag: iTRAQ 8plex 119 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 119. Name: frag: iTRAQ 8plex 121 reporter ion Description: Standard reporter ion for iTRAQ 8Plex 121. TMT: Name: frag: TMT 126 reporter ion Description: Standard reporter ion for TMT 126. Name: frag: TMT 127N reporter ion Description: Standard reporter ion for TMT 127N. Name: frag: TMT 127C reporter ion Description: Standard reporter ion for TMT 127C. Name: frag: TMT 128N reporter ion Description: Standard reporter ion for TMT 128N. Name: frag: TMT 128C reporter ion Description: Standard reporter ion for TMT 128C. Name: frag: TMT 128N reporter ion Description: Standard reporter ion for TMT 128N. Name: frag: TMT 128C reporter ion Description: Standard reporter ion for TMT 128C. Name: frag: TMT 130N reporter ion Description: Standard reporter ion for TMT 130N. Name: frag: TMT 130C reporter ion Description: Standard reporter ion for TMT 130C. Name: frag: TMT 131 reporter ion Description: Standard reporter ion for TMT 131. Name: frag: TMT 126 ETD reporter ion Description: Standard reporter ion for TMT 126 ETD. Name: frag: TMT 127N ETD reporter ion Description: Standard reporter ion for TMT 127N ETD. Name: frag: TMT 127C ETD reporter ion Description: Standard reporter ion for TMT 127C ETD. Name: frag: TMT 128N ETD reporter ion Description: Standard reporter ion for TMT 128N ETD. Name: frag: TMT 128C ETD reporter ion Description: Standard reporter ion for TMT 128C ETD. Name: frag: TMT 129N ETD reporter ion Description: Standard reporter ion for TMT 129N ETD. Name: frag: TMT 129C ETD reporter ion Description: Standard reporter ion for TMT 129C ETD. Name: frag: TMT 130N ETD reporter ion Description: Standard reporter ion for TMT 130N ETD. Name: frag: TMT 130C ETD reporter ion Description: Standard reporter ion for TMT 130C ETD. Name: frag: TMT 131 ETD reporter ion Description: Standard reporter ion for TMT 131 ETD. All should be children of MS:1002307 (fragmentation ion type). Thanks in advance. Best regards, Harald -- *--* *Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail *ger...@ru... www.medizinisches-proteom-center.de [image: RUB Logo] ANNOUNCEMENT de.NBI summer school September 2016: *Analysis of Mass-Spectrometric Data - * *Big Data Bioinformatics in Proteomics and Metabolomics* http://www.denbi.de/index.php/11-training-cat/95-lss2016 |
|
From: mayerg97 <ger...@ru...> - 2016-05-24 13:56:12
|
Hi all, how about the following terms? ************ New terms for neutral losses [Term] id: MS:1002668 name: HPO3 neutral loss def: "Neutral loss of phosphite." [PSI:PI] is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1002669 name: CH4OS neutral loss def: "Neutral loss of methanesulfenic acid." [PSI:PI] is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1002670 name: C3H9N neutral loss def: "Neutral loss of C3H9N." [PSI:PI] is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search ************ New terms for reporter ions. The mass resp. type can be specified in the value slot. [Term] id: MS:1002671 name: frag: iTRAQ 4plex reporter ion def: "Standard reporter ion for iTRAQ 4Plex." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1002672 name: frag: iTRAQ 8plex reporter ion def: "Standard reporter ion for iTRAQ 8Plex." [PSI:PI] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1002673 name: frag: TMT reporter ion def: "Standard reporter ion for TMT." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1002674 name: frag: TMT ETD reporter ion def: "Standard reporter ion for TMT ETD." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002307 ! fragmentation ion type Best regards, Gerhard Am 24.05.2016 um 12:55 schrieb Harald Barsnes: > > Hi Gerhard, > > Thanks for adding the neutral losses CV terms. Would be great if you > could also add CV terms for the following reporter ions. > > > iTRAQ 4plex: > > Name: frag: iTRAQ 4plex 114 reporter ion > Description: Standard reporter ion for iTRAQ 4Plex 114. > > Name: frag: iTRAQ 4plex 115 reporter ion > Description: Standard reporter ion for iTRAQ 4Plex 115. > > Name: frag: iTRAQ 4plex 116 reporter ion > Description: Standard reporter ion for iTRAQ 4Plex 116. > > Name: frag: iTRAQ 4plex 117 reporter ion > Description: Standard reporter ion for iTRAQ 4Plex 117. > > > iTRAQ 8plex: > > Name: frag: iTRAQ 8plex 113 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 113. > > Name: frag: iTRAQ 8plex 114 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 114. > > Name: frag: iTRAQ 8plex 115 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 115. > > Name: frag: iTRAQ 8plex 116 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 116. > > Name: frag: iTRAQ 8plex 117 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 117. > > Name: frag: iTRAQ 8plex 118 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 118. > > Name: frag: iTRAQ 8plex 119 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 119. > > Name: frag: iTRAQ 8plex 121 reporter ion > Description: Standard reporter ion for iTRAQ 8Plex 121. > > > TMT: > > Name: frag: TMT 126 reporter ion > Description: Standard reporter ion for TMT 126. > > Name: frag: TMT 127N reporter ion > Description: Standard reporter ion for TMT 127N. > > Name: frag: TMT 127C reporter ion > Description: Standard reporter ion for TMT 127C. > > Name: frag: TMT 128N reporter ion > Description: Standard reporter ion for TMT 128N. > > Name: frag: TMT 128C reporter ion > Description: Standard reporter ion for TMT 128C. > > Name: frag: TMT 128N reporter ion > Description: Standard reporter ion for TMT 128N. > > Name: frag: TMT 128C reporter ion > Description: Standard reporter ion for TMT 128C. > > Name: frag: TMT 130N reporter ion > Description: Standard reporter ion for TMT 130N. > > Name: frag: TMT 130C reporter ion > Description: Standard reporter ion for TMT 130C. > > Name: frag: TMT 131 reporter ion > Description: Standard reporter ion for TMT 131. > > Name: frag: TMT 126 ETD reporter ion > Description: Standard reporter ion for TMT 126 ETD. > > Name: frag: TMT 127N ETD reporter ion > Description: Standard reporter ion for TMT 127N ETD. > > Name: frag: TMT 127C ETD reporter ion > Description: Standard reporter ion for TMT 127C ETD. > > Name: frag: TMT 128N ETD reporter ion > Description: Standard reporter ion for TMT 128N ETD. > > Name: frag: TMT 128C ETD reporter ion > Description: Standard reporter ion for TMT 128C ETD. > > Name: frag: TMT 129N ETD reporter ion > Description: Standard reporter ion for TMT 129N ETD. > > Name: frag: TMT 129C ETD reporter ion > Description: Standard reporter ion for TMT 129C ETD. > > Name: frag: TMT 130N ETD reporter ion > Description: Standard reporter ion for TMT 130N ETD. > > Name: frag: TMT 130C ETD reporter ion > Description: Standard reporter ion for TMT 130C ETD. > > Name: frag: TMT 131 ETD reporter ion > Description: Standard reporter ion for TMT 131 ETD. > > > All should be children of MS:1002307 (fragmentation ion type). > > > Thanks in advance. > > Best regards, > Harald > -- *--* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> RUB Logo ANNOUNCEMENT de.NBI summer school September 2016: *Analysis of Mass-Spectrometric Data - * *Big Data Bioinformatics in Proteomics and Metabolomics* http://www.denbi.de/index.php/11-training-cat/95-lss2016 |
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From: Juan A. V. <ju...@eb...> - 2016-05-23 13:52:48
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> Begin forwarded message: > > From: Oliver Kohlbacher <oli...@un...> > Subject: [Psi-announce] Bioinformatics hub at ASMS 2016 > Date: 23 May 2016 at 05:07:13 BST > To: Co...@go..., psi...@eb... > > Dear colleagues, > > We are preparing another Bioinformatics Hub at ASMS 2016 in San Antonio, TX. > > Similar to the HUPO 2015 Bioinformatics Hub [http://www.psidev.info/hupo2015-bioinformatics-hub] last year, we intend to create a place where ASMS participants and bioinformatics experts can meet. The objective of this hands-on meeting is to develop and execute original bioinformatics analyses on the publicly available human proteomics data during the conference, facilitated by several leading proteomics informatics groups, and completely open for participation by any and all interested conference attendees. In Ask-The-Experts sessions, proteomics bioinformatics experts and the audience will discuss and answer any hot topic questions in proteomics bioinformatics. > > Goals of the Bioinformatics Hub: > - To provide advice on computational methods and their correct usage to experimentalists > - To come up with novel approaches and ideas to perform integrative proteomics data analysis and interpretation. > - To discuss limitations of existing tools and data processing algorithms. > - To foster collaborative interactions between wet-lab researchers and bioinformaticians. > - To identify gaps in the existing computational mass spectrometry tools, inspiring future work to fill these gaps. > - Networking. > > As a bioinformatics expert, we would be delighted if you could contribute to this effort. > > We would thus be grateful, if you could indicate your availability in the Google form > at http://goo.gl/forms/tt488yl4v7JKWEiE3. > > We would also greatly appreciate if you would forward this email to > other bioinformaticians attending ASMS. > > Thanks a lot > The organizers > (Oliver Kohlbacher, Yassene Mohammed, Juan Antonio Vizcaino, Sue Weintraub) > > --- > Oliver Kohlbacher > Professor, Center for Bioinformatics, Dept. of Computer Science, & Faculty of Medicine > Director, Quantitative Biology Center, University of Tuebingen, Germany > Fellow, Max Planck Institute for Developmental Biology > > email oli...@un... / oli...@tu... > WWW kohlbacherLab.org twitter @OKohlbacher > phone +49 7071 29 70457 fax +49 7071 29 5152 > > > _______________________________________________ > Psi-announce mailing list > Psi...@eb... > https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce |
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From: mayerg97 <ger...@ru...> - 2016-05-23 10:28:45
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Dear proteomics community,
attached there's the release candidate 3.89.0_rc1 of the psi-ms.obo file.
New CV terms in version 3.89.0_rc1 of psi-ms.obo:
=================================================
************ New terms for fragment ions with neutral losses
[Term]
id: MS:1002668
name: frag: a ion - H3PO4
def: "Fragmentation information, type of product: a ion with a loss of
H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002669
name: frag: a ion - HPO3
def: "Fragmentation information, type of product: a ion with a loss of
HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002670
name: frag: a ion - CH4OS
def: "Fragmentation information, type of product: a ion with a loss of
CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002671
name: frag: a ion - C3H9N
def: "Fragmentation information, type of product: a ion with a loss of
C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002672
name: frag: b ion - H3PO4
def: "Fragmentation information, type of product: b ion with a loss of
H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002673
name: frag: b ion - HPO3
def: "Fragmentation information, type of product: b ion with a loss of
HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002674
name: frag: b ion - CH4OS
def: "Fragmentation information, type of product: b ion with a loss of
CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002675
name: frag: b ion - C3H9N
def: "Fragmentation information, type of product: b ion with a loss of
C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002676
name: frag: c ion - H3PO4
def: "Fragmentation information, type of product: c ion with a loss of
H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002677
name: frag: c ion - HPO3
def: "Fragmentation information, type of product: c ion with a loss of
HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002678
name: frag: c ion - CH4OS
def: "Fragmentation information, type of product: c ion with a loss of
CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002679
name: frag: c ion - C3H9N
def: "Fragmentation information, type of product: c ion with a loss of
C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002680
name: frag: x ion - H3PO4
def: "Fragmentation information, type of product: x ion with a loss of
H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002681
name: frag: x ion - HPO3
def: "Fragmentation information, type of product: x ion with a loss of
HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002682
name: frag: x ion - CH4OS
def: "Fragmentation information, type of product: x ion with a loss of
CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002683
name: frag: x ion - C3H9N
def: "Fragmentation information, type of product: x ion with a loss of
C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002684
name: frag: y ion - H3PO4
def: "Fragmentation information, type of product: y ion with a loss of
H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002685
name: frag: y ion - HPO3
def: "Fragmentation information, type of product: y ion with a loss of
HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002686
name: frag: y ion - CH4OS
def: "Fragmentation information, type of product: y ion with a loss of
CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002687
name: frag: y ion - C3H9N
def: "Fragmentation information, type of product: y ion with a loss of
C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002688
name: frag: z ion - H3PO4
def: "Fragmentation information, type of product: z ion with a loss of
H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002689
name: frag: z ion - HPO3
def: "Fragmentation information, type of product: z ion with a loss of
HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002690
name: frag: z ion - CH4OS
def: "Fragmentation information, type of product: z ion with a loss of
CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002691
name: frag: z ion - C3H9N
def: "Fragmentation information, type of product: z ion with a loss of
C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
************ New terms for precursor ions with neutral losses
[Term]
id: MS:1002692
name: frag: precursor ion - H3PO4
def: "Fragmentation information, type of product: precursor ion with a
loss of H3PO4." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002693
name: frag: precursor ion - HPO3
def: "Fragmentation information, type of product: precursor ion with a
loss of HPO3." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002694
name: frag: precursor ion - CH4OS
def: "Fragmentation information, type of product: precursor ion with a
loss of CH4OS." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
[Term]
id: MS:1002695
name: frag: precursor ion - C3H9N
def: "Fragmentation information, type of product: precursor ion with a
loss of C3H9N." [PSI:PI]
is_a: MS:1002307 ! fragmentation ion type
Changed CV terms in version 3.89.0_rc1 of psi-ms.obo:
=====================================================
************ Changed the regular expression to allow null for the
interaction position
[Term]
id: MS:1002665
name: regular expression for protein interaction scores derived from
cross-linking
def:
"([:digit:]+[.][a|b]:([:digit:]+|null):[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\})"
[PSI:PI]
is_a: MS:1002479 ! regular expression
Best Regards,
Gerhard
--
*--*
*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*
*PhD student*
*Medizinisches Proteom-Center*
*DEPARTMENT Medical Bioinformatics*
*Building *ZKF E.049a | Universitätsstraße 150 | D-44801 Bochum
*Fon *+49 (0)234 32-21006 | *Fax *+49 (0)234 32-14554
*E-mail***ger...@ru... <mailto:ger...@ru...>
www.medizinisches-proteom-center.de
<http://www.medizinisches-proteom-center.de/>
RUB Logo
ANNOUNCEMENT de.NBI summer school September 2016:
*Analysis of Mass-Spectrometric Data - *
*Big Data Bioinformatics in Proteomics and Metabolomics*
http://www.denbi.de/index.php/11-training-cat/95-lss2016
|
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From: Yasset Perez-R. <not...@gi...> - 2016-05-23 09:50:38
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@lgatto The only software producing mztab are the internal pipeline of PRIDE and OpenMS is working also on that. WE will have soon examples from OpenMS. @timosachsenberg can you provide us an example of mztab with PEP section. Ready to be use. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzTab/issues/23#issuecomment-220936074 |
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From: Laurent G. <not...@gi...> - 2016-05-21 21:53:54
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There seems to be no example containing a `PEP` section - would it be possible to add one? --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzTab/issues/23 |
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From: Mathias W. <not...@gi...> - 2016-05-20 09:42:12
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Merged #22. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/qcML-development/pull/22#event-666914959 |
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From: Mathias W. <not...@gi...> - 2016-05-20 09:40:20
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Merged #21. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/qcML-development/pull/21#event-666913018 |
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From: Gerhard M. <not...@gi...> - 2016-05-19 14:44:40
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[CV-terms for PTM, PSM, peptide, protein and protein-group scores.docx](https://github.com/HUPO-PSI/mzIdentML/files/272801/CV-terms.for.PTM.PSM.peptide.protein.and.protein-group.scores.docx) --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/25#issuecomment-220346235 |
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From: andrewrobertjones <not...@gi...> - 2016-05-18 15:40:36
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@lutzfischer is going to update the CV with the n-term specs. Agree for now the theoretical case raised by @timosachsenberg is not needed at the moment --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/13#issuecomment-220067340 |
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From: andrewrobertjones <not...@gi...> - 2016-05-18 15:40:25
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Closed #13. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/13#event-664590304 |
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From: andrewrobertjones <not...@gi...> - 2016-05-18 15:36:56
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Closed #19. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/19#event-664584743 |
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From: andrewrobertjones <not...@gi...> - 2016-05-18 15:36:51
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Think this is solved, please re-open if anything was missed. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/19#issuecomment-220066188 |
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From: andrewrobertjones <not...@gi...> - 2016-05-18 15:33:10
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Overall agreement on call that this looks okay for now. Lutz will make proposal for CV terms for his software. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/24#issuecomment-220065055 |
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From: andrewrobertjones <not...@gi...> - 2016-05-18 15:21:13
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Closed #28. --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/28#event-664560982 |
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From: andrewrobertjones <not...@gi...> - 2016-05-18 15:21:06
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We agree that either Unimod or XLMOD CV is fine --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/28#issuecomment-220061087 |
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From: Jones, A. <And...@li...> - 2016-05-18 14:57:50
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Hi all, Apologies I may be a few minutes late, please start without me – taking a look through the issues etc. Best wishes Andy From: Jones, Andy Sent: 17 May 2016 09:31 To: 'psi...@li...' <psi...@li...> Cc: 'eug...@tu...' <eug...@tu...>; 'le...@im...' <le...@im...>; 'Andrea Sinz' <and...@ph...>; 'Robert Chalkley' <cha...@cg...>; 'eli...@ug...' <eli...@ug...>; 'ju...@ed...' <ju...@ed...>; 'sul...@ug...' <sul...@ug...> Subject: RE: Cross-linking discussions at PSI meeting Hi all, Just confirming we will have the call tomorrow at 4pm UK, 5pm EU, 8am California to discuss progress on cross-linking in mzid 1.2. Agenda: - Update on CV (Lutz – can you join the call, and/or send an update in advance - Update on example files (Lutz/Eugen) and tests against the validator. Please raise an issue if have any problems with the validator - Work through issues on list: https://github.com/HUPO-PSI/mzIdentML/issues I feel we are almost complete on all other mzid 1.2 issues, and cross-linking is the one outstanding features. As such, I would appreciate a push from everyone at this point to get this done, so we can submit the specifications to the document process. Best wishes Andy Numbers: + UK: 0808 109 5644 + US: 877-420-0272 + Belgium: 0800 509 80 + Germany: 0800 101 2079 + Switzerland: 0800 000 860 + Generic international: +44 (0) 20 8322 2500 (UK number) Access code: 297427 # From: Jones, Andy Sent: 11 May 2016 16:56 To: 'psi...@li...' <psi...@li...<mailto:psi...@li...>> Cc: 'eug...@tu...' <eug...@tu...<mailto:eug...@tu...>>; 'le...@im...' <le...@im...<mailto:le...@im...>>; 'Andrea Sinz' <and...@ph...<mailto:and...@ph...>>; 'Robert Chalkley' <cha...@cg...<mailto:cha...@cg...>>; 'eli...@ug...' <eli...@ug...<mailto:eli...@ug...>>; 'ju...@ed...' <ju...@ed...<mailto:ju...@ed...>>; 'sul...@ug...' <sul...@ug...<mailto:sul...@ug...>> Subject: RE: Cross-linking discussions at PSI meeting Hi all (crosslinking people specifically), We would like to schedule the next crosslinking-mzid call for Wed 18th at 4pm (UK); 5pm EU – please can you let me know if this suits. Best wishes Andy From: Jones, Andy Sent: 04 May 2016 17:06 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: RE: Cross-linking discussions at PSI meeting Hi all, Brief summary from the call: 1. Agreed that expMassToCharge, calcMassToCharge and chargeState should be identical for alpha and beta PSMs, reflecting the overall values for the cross-linked molecules; a. Also agreed that for consensus spectrum approach, there should be one SpectrumIdentificationItem per peptide chain identified, we acknowledge potential for some loss of information, but probably impossible to second guess everything that people want to encode 2. General agreement over my proposal for interaction scores as per issue pdf 3. Agreed for Lutz to make a provisional release of a very simple CV e.g. XLMOD.1.0.1.csv; and have a second working copy where ideas can be developed; Detail can be added over time, as people need specific terms 4. Proteogenomics – Agreed to move chromosome name and strand to DBSequence (protein-level), also move Genome reference version to DBSequence; Remove “peptide start position on chromosome” as redundant info, this is not needed for the encoding 5. Decide to leave the issue open for now for people to vote on, not enough people on the call to take a decision Proposed date for next call, same time slot next Wed 11th May – please let me know if you can make it. Plan to discuss mzid items, not including cross-linking next week. Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 04 May 2016 14:27 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting Hi all, The main items to work through today are as follows: 1. The XL encoding with consensus spectra, and more generally what values should go in expMassToCharge, calcMassToCharge and chargeState: https://github.com/HUPO-PSI/mzIdentML/issues/19, as we identified a flaw in the proposed specs a. For background see Section 5.2.8 of the spec doc: https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_2/mzIdentML1%202-draft.docx 2. How to encode protein-level interaction evidence: https://github.com/HUPO-PSI/mzIdentML/issues/24 3. Any issues around CV of reagents: https://github.com/HUPO-PSI/mzIdentML/blob/master/cv/XLMOD.csv. Looks like it hasn’t been updated since last week – Lutz, any developments here? Time permitting, I would like sign off one or two non-XL issues: 4. Proteogenomics: https://github.com/HUPO-PSI/mzIdentML/issues/4; Specifically encoding of genome reference version; and whether to keep CV term for “peptide start on chromosome” since info is redundant 5. Multiple search engine encoding: https://github.com/HUPO-PSI/mzIdentML/issues/5 Speak in 1.5 hours, Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 03 May 2016 14:58 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting Hi all, As a reminder, we will have our next mzid 1.2 call tomorrow at 4pm UK time/5pm EU/8am California for those of you who can join: http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160504T16&p1=301&ah=1 The dial in details are as usual (below) – Juan, is there someone at the EBI who can start the call for us? Agenda: 1. XL encoding and CV issues (before the call I will update issues and documentation in GitHub) 2. Work through other mzid 1.2 issues (time permitting): https://github.com/HUPO-PSI/mzIdentML/issues 3. Any other business Best wishes Andy Numbers: + UK: 0808 109 5644 + US: 877-420-0272 + Belgium: 0800 509 80 + Germany: 0800 101 2079 + Switzerland: 0800 000 860 + Generic international: +44 (0) 20 8322 2500 (UK number) Access code: 297427 # From: Jones, Andy Sent: 28 April 2016 15:37 To: 'Jones, Andy' <And...@li...<mailto:And...@li...>>; psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: RE: Cross-linking discussions at PSI meeting Summary of items we will discuss on the call (30 mins time): 1. Overview of encoding as written in spec doc: https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_2/mzIdentML1%202-draft.docx (section 5.2.8 and Figure 3 and Figure 4) a. Note Figure 4 is subject to change following our discussions 2. Work through issues flagged here, particularly those mentioned by Lutz: https://github.com/HUPO-PSI/mzIdentML/issues/2; a. For this we will also need to look at the proposed XL CV: https://github.com/HUPO-PSI/mzIdentML/blob/master/cv/XLMOD.csv 3. Action points towards getting the XL part of mzid 1.2 complete Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 27 April 2016 10:22 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting Hi all, This is to confirm that we will have a call at 4pm UK, 5pm EU, 8am California: http://www.timeanddate.com/worldclock/fixedtime.html?msg=PSI-PI+call+on+crosslinking&iso=20160428T16&p1=301&ah=1 The main topic for discussion will be encoding cross-linking in mzIdentML 1.2. Current issues with mzIdentML 1.2 are being discussed on GitHub here: https://github.com/HUPO-PSI/mzIdentML/issues, I will update it with open issues around cross-linking by tomorrow. The current version of the specifications are here (rather long I’m afraid) along with a powerpoint explaining the encodings for new features: https://github.com/HUPO-PSI/mzIdentML/tree/master/specification_document/specdoc1_2 If Lutz is able to create a CV file for reagents before the call, we will also post that online for discussions. Best wishes Andy Numbers: + UK: 0808 109 5644 + US: 877-420-0272 + Belgium: 0800 509 80 + Germany: 0800 101 2079 + Switzerland: 0800 000 860 + Generic international: +44 (0) 20 8322 2500 (UK number) Access code: 297427 # From: Jones, Andy Sent: 19 April 2016 15:56 To: tobias <to...@eb...<mailto:to...@eb...>> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; sul...@ug...<mailto:sul...@ug...>; ju...@ed...<mailto:ju...@ed...>; eli...@ug...<mailto:eli...@ug...>; Lutz Fischer <lfi...@st...<mailto:lfi...@st...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; Juan Antonio Vizcaino <ju...@eb...<mailto:ju...@eb...>>; Yasset Perez-Riverol <yp...@eb...<mailto:yp...@eb...>>; psi...@li...<mailto:psi...@li...> Subject: Cross-linking discussions at PSI meeting Hi all, This email is addressed to those who participated in the XL session at PSI today, plus Lutz and Robert (and plus Yasset for GitHub issues). Please forward this on to others who should be consulted. I have also copied to the PSI-PI list. The major outcomes from today are as follows: 1. General agreement that we are nearly there with the mzid 1.2 encoding of XL info. 2. Plan for Lutz to maintain (via mzIdentML GitHub for example), a separate CV of crosslinker reagents, based off the attached sheet (converted to CSV format, with unique IDs per row e.g. XL:0001, XL:0002, more discussion needed to finalise format) 3. Some additions to mzid 1.2 to cover: - cases of combined evidence from multiple input spectra (L v H isotopes; ETD+HCD; MS3 etc) to make an identification (not post-processing but intrinsic to the ID mechanism) - Adding protein-level interaction evidence - Re-using additions already proposed in mzid 1.2 for mod or XL localization ambiguity 4. No major interest at this stage to encode XL info in mztab, we may do this at our side following same model as mzid 1.2 5. Plan for wider project over medium to long term to write a cross-linking standards paper, including mzid 1.2 plus a minimum reporting guidelines doc (Juri / Alexander to progress this), with wider authorship 6. We will role these changes into mzid 1.2 specifications, and publish that paper separately (submitted in the short term). For those that contribute example files or major input of the specs, I will invite to join the author list of that paper. I have started to write this up in the mzid 1.2 specification document (attached here and committed to our GitHub) - see pages 20-23), and an XML snippet for how the protein interaction part will look. ACTION items: - We discussed Lutz updating the xi export examples to include protein interaction scores, following our proposed spec - Alexander and Eugen to update the examples exported from OpenMS and add to the mzid GitHub (please email Yasset - cc'd to get write access to the GitHub) - Ideally, would be great if the Edinburgh visualisation software could read the mzid 1.2 files to see if all info is really covered - Andy to continue cleaning and updating specification document I would like to propose a conference call to progress this for 4pm UK/5pm Europe on Thurs 28th April - please reply to let me know if you can make it. best wishes Andy |
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From: Jones, A. <And...@li...> - 2016-05-17 08:34:13
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Hi all, Just confirming we will have the call tomorrow at 4pm UK, 5pm EU, 8am California to discuss progress on cross-linking in mzid 1.2. Agenda: - Update on CV (Lutz – can you join the call, and/or send an update in advance - Update on example files (Lutz/Eugen) and tests against the validator. Please raise an issue if have any problems with the validator - Work through issues on list: https://github.com/HUPO-PSI/mzIdentML/issues I feel we are almost complete on all other mzid 1.2 issues, and cross-linking is the one outstanding features. As such, I would appreciate a push from everyone at this point to get this done, so we can submit the specifications to the document process. Best wishes Andy Numbers: + UK: 0808 109 5644 + US: 877-420-0272 + Belgium: 0800 509 80 + Germany: 0800 101 2079 + Switzerland: 0800 000 860 + Generic international: +44 (0) 20 8322 2500 (UK number) Access code: 297427 # From: Jones, Andy Sent: 11 May 2016 16:56 To: 'psi...@li...' <psi...@li...> Cc: 'eug...@tu...' <eug...@tu...>; 'le...@im...' <le...@im...>; 'Andrea Sinz' <and...@ph...>; 'Robert Chalkley' <cha...@cg...>; 'eli...@ug...' <eli...@ug...>; 'ju...@ed...' <ju...@ed...>; 'sul...@ug...' <sul...@ug...> Subject: RE: Cross-linking discussions at PSI meeting Hi all (crosslinking people specifically), We would like to schedule the next crosslinking-mzid call for Wed 18th at 4pm (UK); 5pm EU – please can you let me know if this suits. Best wishes Andy From: Jones, Andy Sent: 04 May 2016 17:06 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: RE: Cross-linking discussions at PSI meeting Hi all, Brief summary from the call: 1. Agreed that expMassToCharge, calcMassToCharge and chargeState should be identical for alpha and beta PSMs, reflecting the overall values for the cross-linked molecules; a. Also agreed that for consensus spectrum approach, there should be one SpectrumIdentificationItem per peptide chain identified, we acknowledge potential for some loss of information, but probably impossible to second guess everything that people want to encode 2. General agreement over my proposal for interaction scores as per issue pdf 3. Agreed for Lutz to make a provisional release of a very simple CV e.g. XLMOD.1.0.1.csv; and have a second working copy where ideas can be developed; Detail can be added over time, as people need specific terms 4. Proteogenomics – Agreed to move chromosome name and strand to DBSequence (protein-level), also move Genome reference version to DBSequence; Remove “peptide start position on chromosome” as redundant info, this is not needed for the encoding 5. Decide to leave the issue open for now for people to vote on, not enough people on the call to take a decision Proposed date for next call, same time slot next Wed 11th May – please let me know if you can make it. Plan to discuss mzid items, not including cross-linking next week. Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 04 May 2016 14:27 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting Hi all, The main items to work through today are as follows: 1. The XL encoding with consensus spectra, and more generally what values should go in expMassToCharge, calcMassToCharge and chargeState: https://github.com/HUPO-PSI/mzIdentML/issues/19, as we identified a flaw in the proposed specs a. For background see Section 5.2.8 of the spec doc: https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_2/mzIdentML1%202-draft.docx 2. How to encode protein-level interaction evidence: https://github.com/HUPO-PSI/mzIdentML/issues/24 3. Any issues around CV of reagents: https://github.com/HUPO-PSI/mzIdentML/blob/master/cv/XLMOD.csv. Looks like it hasn’t been updated since last week – Lutz, any developments here? Time permitting, I would like sign off one or two non-XL issues: 4. Proteogenomics: https://github.com/HUPO-PSI/mzIdentML/issues/4; Specifically encoding of genome reference version; and whether to keep CV term for “peptide start on chromosome” since info is redundant 5. Multiple search engine encoding: https://github.com/HUPO-PSI/mzIdentML/issues/5 Speak in 1.5 hours, Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 03 May 2016 14:58 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting Hi all, As a reminder, we will have our next mzid 1.2 call tomorrow at 4pm UK time/5pm EU/8am California for those of you who can join: http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160504T16&p1=301&ah=1 The dial in details are as usual (below) – Juan, is there someone at the EBI who can start the call for us? Agenda: 1. XL encoding and CV issues (before the call I will update issues and documentation in GitHub) 2. Work through other mzid 1.2 issues (time permitting): https://github.com/HUPO-PSI/mzIdentML/issues 3. Any other business Best wishes Andy Numbers: + UK: 0808 109 5644 + US: 877-420-0272 + Belgium: 0800 509 80 + Germany: 0800 101 2079 + Switzerland: 0800 000 860 + Generic international: +44 (0) 20 8322 2500 (UK number) Access code: 297427 # From: Jones, Andy Sent: 28 April 2016 15:37 To: 'Jones, Andy' <And...@li...<mailto:And...@li...>>; psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: RE: Cross-linking discussions at PSI meeting Summary of items we will discuss on the call (30 mins time): 1. Overview of encoding as written in spec doc: https://github.com/HUPO-PSI/mzIdentML/blob/master/specification_document/specdoc1_2/mzIdentML1%202-draft.docx (section 5.2.8 and Figure 3 and Figure 4) a. Note Figure 4 is subject to change following our discussions 2. Work through issues flagged here, particularly those mentioned by Lutz: https://github.com/HUPO-PSI/mzIdentML/issues/2; a. For this we will also need to look at the proposed XL CV: https://github.com/HUPO-PSI/mzIdentML/blob/master/cv/XLMOD.csv 3. Action points towards getting the XL part of mzid 1.2 complete Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 27 April 2016 10:22 To: psi...@li...<mailto:psi...@li...> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; Andrea Sinz <and...@ph...<mailto:and...@ph...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; eli...@ug...<mailto:eli...@ug...>; ju...@ed...<mailto:ju...@ed...>; sul...@ug...<mailto:sul...@ug...> Subject: Re: [Psidev-pi-dev] Cross-linking discussions at PSI meeting Hi all, This is to confirm that we will have a call at 4pm UK, 5pm EU, 8am California: http://www.timeanddate.com/worldclock/fixedtime.html?msg=PSI-PI+call+on+crosslinking&iso=20160428T16&p1=301&ah=1 The main topic for discussion will be encoding cross-linking in mzIdentML 1.2. Current issues with mzIdentML 1.2 are being discussed on GitHub here: https://github.com/HUPO-PSI/mzIdentML/issues, I will update it with open issues around cross-linking by tomorrow. The current version of the specifications are here (rather long I’m afraid) along with a powerpoint explaining the encodings for new features: https://github.com/HUPO-PSI/mzIdentML/tree/master/specification_document/specdoc1_2 If Lutz is able to create a CV file for reagents before the call, we will also post that online for discussions. Best wishes Andy Numbers: + UK: 0808 109 5644 + US: 877-420-0272 + Belgium: 0800 509 80 + Germany: 0800 101 2079 + Switzerland: 0800 000 860 + Generic international: +44 (0) 20 8322 2500 (UK number) Access code: 297427 # From: Jones, Andy Sent: 19 April 2016 15:56 To: tobias <to...@eb...<mailto:to...@eb...>> Cc: eug...@tu...<mailto:eug...@tu...>; le...@im...<mailto:le...@im...>; sul...@ug...<mailto:sul...@ug...>; ju...@ed...<mailto:ju...@ed...>; eli...@ug...<mailto:eli...@ug...>; Lutz Fischer <lfi...@st...<mailto:lfi...@st...>>; Robert Chalkley <cha...@cg...<mailto:cha...@cg...>>; Juan Antonio Vizcaino <ju...@eb...<mailto:ju...@eb...>>; Yasset Perez-Riverol <yp...@eb...<mailto:yp...@eb...>>; psi...@li...<mailto:psi...@li...> Subject: Cross-linking discussions at PSI meeting Hi all, This email is addressed to those who participated in the XL session at PSI today, plus Lutz and Robert (and plus Yasset for GitHub issues). Please forward this on to others who should be consulted. I have also copied to the PSI-PI list. The major outcomes from today are as follows: 1. General agreement that we are nearly there with the mzid 1.2 encoding of XL info. 2. Plan for Lutz to maintain (via mzIdentML GitHub for example), a separate CV of crosslinker reagents, based off the attached sheet (converted to CSV format, with unique IDs per row e.g. XL:0001, XL:0002, more discussion needed to finalise format) 3. Some additions to mzid 1.2 to cover: - cases of combined evidence from multiple input spectra (L v H isotopes; ETD+HCD; MS3 etc) to make an identification (not post-processing but intrinsic to the ID mechanism) - Adding protein-level interaction evidence - Re-using additions already proposed in mzid 1.2 for mod or XL localization ambiguity 4. No major interest at this stage to encode XL info in mztab, we may do this at our side following same model as mzid 1.2 5. Plan for wider project over medium to long term to write a cross-linking standards paper, including mzid 1.2 plus a minimum reporting guidelines doc (Juri / Alexander to progress this), with wider authorship 6. We will role these changes into mzid 1.2 specifications, and publish that paper separately (submitted in the short term). For those that contribute example files or major input of the specs, I will invite to join the author list of that paper. I have started to write this up in the mzid 1.2 specification document (attached here and committed to our GitHub) - see pages 20-23), and an XML snippet for how the protein interaction part will look. ACTION items: - We discussed Lutz updating the xi export examples to include protein interaction scores, following our proposed spec - Alexander and Eugen to update the examples exported from OpenMS and add to the mzid GitHub (please email Yasset - cc'd to get write access to the GitHub) - Ideally, would be great if the Edinburgh visualisation software could read the mzid 1.2 files to see if all info is really covered - Andy to continue cleaning and updating specification document I would like to propose a conference call to progress this for 4pm UK/5pm Europe on Thurs 28th April - please reply to let me know if you can make it. best wishes Andy |
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From: Juan A. V. <not...@gi...> - 2016-05-16 09:00:09
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I think it is perfectly fine --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/4#issuecomment-219380210 |
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